The process of drug discovery is presently undergoing a fundamental revolution as the era of functional genomics comes of age. The term “functional genomics” applies to an approach utilising bioinformatics tools to ascribe function to protein sequences of interest. Such tools are becoming increasingly necessary as the speed of generation of sequence data is rapidly outpacing the ability of research laboratories to assign functions to these protein sequences.
As bioinformatics tools increase in potency and in accuracy, these tools are rapidly replacing the conventional techniques of biochemical characterisation. Indeed, the advanced bioinformatics tools used in identifying the present invention are now capable of outputting results in which a high degree of confidence can be placed.
Various institutions and commercial organisations are examining sequence data as they become available and significant discoveries are being made on an on-going basis. However, there remains a continuing need to identify and characterise further genes and the polypeptides that they encode, as targets for research and for drug discovery.
Recently, a remarkable tool for the evaluation of sequences of unknown function has been developed by the Applicant for the present invention. This tool is a database system, termed the Biopendium search database, that is the subject of WO01/69507. This database system consists of an integrated data resource created using proprietary technology and containing information generated from an all-by-all comparison of all available protein or nucleic acid sequences.
The aim behind the integration of these sequence data from separate data resources is to combine as much data as possible, relating both to the sequences themselves and to information relevant to each sequence, into one integrated resource. All the available data relating to each sequence, including data on the three-dimensional structure of the encoded protein, if this is available, are integrated together to make best use of the information that is known about each sequence and thus to allow the most educated predictions to be made from comparisons of these sequences. The annotation that is generated in the database and which accompanies each sequence entry imparts a biologically relevant context to the sequence information.
This data resource has made possible the accurate prediction of protein function from sequence alone. Using conventional technology, this is only possible for proteins that exhibit a high degree of sequence identity (above about 20%-30% identity) to other proteins in the same functional family. Accurate predictions are not possible for proteins that exhibit a very low degree of sequence homology to other related proteins of known function.
Signal Peptide-Containing Proteins
The ability of cells to make and secrete extracellular proteins is central to many biological processes. Enzymes, growth factors, extracellular matrix proteins and signaling molecules are all secreted by cells. This is through fusion of a secretory vesicle with the plasma membrane. In most cases, but not all, proteins are directed to the endoplasmic reticulum and into secretory vesicles by a signal peptide. Signal peptides are cis-acting sequences that affect the transport of polypeptide chains from the cytoplasm to a membrane bound compartment such as a secretory vesicle. Polypeptides that are targeted to the secretory vesicles are either secreted into the extracellular matrix or are retained in the plasma membrane. The polypeptides that are retained in the plasma membrane will have one or more transmembrane domains. Examples of signal peptide containing proteins that play a central role in the functioning of a cell are cytokines, hormones, extracellular matrix proteins, adhesion molecules, receptors, proteases, and growth and differentiation factors.
Immunoglobulin Domain-Containing Cell Surface Recognition Molecules
Immunoglobulin domain-containing cell surface recognition molecules have been shown to play a role in diverse physiological functions, many of which can play a role in disease processes. Alteration of their activity is a means to alter the disease phenotype and as such identification of novel immunoglobulin domain-containing cell surface recognition molecules is highly relevant as they may play a role in many diseases, particularly inflammatory disease, oncology, and cardiovascular disease. Immunoglobulin domain-containing cell surface recognition molecules are involved in a range of biological processes, including: embryogenesis (Martin-Bermudo, M. D. et al, Development. 2000 127(12):2607-15; Chen, L. M., et al., J. Neurosci. 2000 20(10):3776-84; Zweegman, S., et al, Exp Hematol. 2000 28(4):401-10; Darribere, T., et al., Biol Cell. 2000 92(1):5-25), maintenance of tissue integrity (Eckes, B., et al., J Cell Sci. 2000 113(Pt 13):2455-2462; Buckwalter, J. A., et al., Instr Course Lect. 2000 49:481-9; Frenette, P. S., et al., J Exp Med. 2000 191(8):1413-22; Delmas, V., et al, Dev Biol. 1999 216(2):491-506; Humphries, M. J., et al., Trends Pharmacol Sci. 2000 21(1):29-32; Miosge, N., et al, Lab Invest. 1999 79(12):1591-9; Nagaoka T, et al. Am J Pathol 2000 July 157:1 237-47; Nwariaku F E, et al. J Trauma 1995 39(2): 285-8; Zhu X, et al. Zhonghua Zheng Xing Shao Shang Wai Ke Za Zhi 1999 15(1): 53-5), leukocyte extravasation/inflammation (Lim, L. H., et al. Am J Respir Cell Mol. Biol. 2000 22(6):693-701; Johnston, B., et al., Microcirculation. 2000 7(2):109-18; Mertens, A. V., et al., Clin Exp Allergy. 1993 23(10):868-73; Chcialowski, A., et al., Pol Merkuriusz Lek. 2000 7(43):13-7; Rojas, A. I., et al, Crit Rev Oral Biol Med. 1999 10(3):337-58; Marinova-Mutafchieva, L., et al., Arthritis Rheum. 2000 43(3):638-44; Vijayan, K. V., et al, J Clin Invest. 2000 105(6):793-802; Currie, A. J., et al,. J. Immunol. 2000 164(7):3878-86; Rowin, M. E., et al., Inflammation. 2000 24(2):157-73; Johnston, B., et al., J. Immunol. 2000 164(6):3337-44; Gerst, J. L., et al., J Neurosci Res. 2000 59(5):680-4; Kagawa, T. F., et al., Proc Natl Acad Sci USA. 2000 97(5):2235-40; Hillan, K. J., et al., Liver. 1999 9(6):509-18; Panes, J., 1999 22(10):514-24; Arao, T., et al., J Clin Endocrinol Metab. 2000 85(1):382-9; Souza, H. S., et al., Gut. 1999 45(6):856-63; Grunstein, M. M., et al., Am J Physiol Lung Cell Mol Physiol. 2000 278(6):L1154-63; Mertens, A. V., et al., Clin Exp Allergy. 1993 23(10):868-73; Berends, C., et al., Clin Exp Allergy. 1993 23(11):926-33; Femvik, E., et al., Inflammation. 2000 24(1):73-87; Bocchino, V., et al., J Allergy Clin Immunol. 2000 105(1 Pt 1):65-70; Jones S C, et al, Gut 1995 36(5):724-30; Liu C M, et al, Ann Allergy Asthma Immunol 1998 81(2):176-80; McMurray R W Semin Arthritis Rheum 1996 25(4):215-33; Takahashi H, et al Eur J Immunol 1992 22(11): 2879-85; Carlos T, et al J Heart Lung Transplant 1992 11(6): 1103-8; Fabrega E, et al, Transplantation 2000 69(4): 569-73; Zohrens G, et al, Hepatology 1993 18(4): 798-802; Montefort S, et al. Am J Respir Crit Care Med 1994 149(5): 1149-52), oncogenesis (Orr, F. W., et al., Cancer. 2000 88(S12):2912-2918; Zeller, W., et al., J Hematother Stem Cell Res. 1999 8(5):539-46; Okada, T., et al., Clin Exp Metastasis. 1999 17(7):623-9; Mateo, V., et al., Nat Med. 1999 5(11):1277-84; Yamaguchi, K., et al., J Exp Clin Cancer Res. 2000 19(1):113-20; Maeshima, Y., et al., J Biol. Chem. 2000 275(28):21340-8; Van Waes, C., et al., Int J Oncol. 2000 16(6):1189-95; Damiano, J. S., et al., Leuk Lymphoma. 2000 38(1-2):71-81; Seflor, R. E., et al., Cancer Metastasis Rev. 1999 18(3):359-75; Shaw, L. M., J Mammary Gland Biol Neoplasia. 1999 4(4):367-76; Weyant, M. J., et al., Clin Cancer Res. 2000 6(3):949-56), angiogenesis (Koch A E, et al Nature 1995 376 (6540): 517-9; Wagener C & Ergun S. Exp Cell Res 2000 261(1): 19-24; Ergun S, et al. Mol Cell 2000 5(2): 311-20), bone resorption (Hartman G D, & Duggan M E. Expert Opin Investig Drugs 2000 9(6): 1281-91; Tanaka Y, et al. J Bone Miner Res 1995 10(10): 1462-9; Lark M W, et al. J Pharmacol Exp Ther 1999 291(2): 612-7; Raynal C, et al. Endocrinology 1996 137(6):2347-54; Ilvesaro J M, et al. Exp Cell Res 1998 242(1): 75-83), neurological dysfunction (Ossege L M, et al. Int Immunopharmacol 2001 1:1085-100; Bitsch A, et al, Stroke 1998 29:2129-35; Iadecola C & Alexander M. Curr Opin Neurol 2001 14:89-94; Becker K, et al Stroke 2001 32(1): 206-11; Relton J K, et al Stroke 2001 32(1): 199-205; Hamada Y, et al J Neurochem 1996 66:1525-31), thrombogenesis (Wang, Y. G., et al., J Physiol (Lond). 2000 526(Pt 1):57-68; Matsuno, H., et al., Nippon Yakurigaku Zasshi. 2000 115(3):143-50; Eliceiri, B. P., et al., Cancer J Sci Am. 2000 6(Suppl 3):S245-9; von Beckerath, N., et al., Blood. 2000 95(11):3297-301; Topol, E. J., et al., Am Heart J. 2000 139(6):927-33; Kroll, H., et al., Thromb Haemost. 2000 83(3):392-6), and invasion/adherence of bacterial pathogens to the host cell (Dersch P, et al. EMBO J 1999 18(5): 1199-1213).
The detailed characterisation of the structure and function of several immunoglobulin-domain containing cell surface recognition molecule families has led to active programs by a number of pharmaceutical companies to develop modulators for use in the treatment of diseases involving inflammation, oncology, neurology, immunology and cardiovascular function. Immunoglobulin domain containing cell surface recognition molecules are involved in virtually every aspect of biology from embryogenesis to apoptosis. They are essential to the structural integrity and homeostatic functioning of most tissues. It is therefore not surprising that defects in immunoglobulin domain containing cell surface recognition molecules cause disease and that many diseases involve modulation of immunoglobulin domain containing cell surface recognition molecule function. The members of this family are described below in Table 1.
The Immunoglobulin domain containing cell surface recognition molecule family in fact contains several distinct families. Of these families, some are of particular pharmaceutical interest due to small molecule tractibility. They include:                1. The immunoglobulin adhesion molecules represent the counter receptors for the integrins and includes the intracellular adhesion molecules (ICAMs) and vascular cell adhesion molecules (VCAMs). Members are composed of variable numbers of globular, immunoglobulin-like, extracellular domains. Some members of the family, for example, PECAM-1 (CD31) and NCAM, mediate homotypic adhesion. Some members of the family, for example ICAM-1 and VCAM-1, mediate adhesion via interactions with integrins.        2. Cell surface growth factor receptors. Growth factors are extracellular and in order to exert a biological effect they interact with specific, high affinity receptors located on the plasma membranes of target cells. The molecular characterisation of a variety of different growth factor receptors revealed that they fall into defined families; the tyrosine kinase receptors, G-protein associated seven transmembrane receptors, and the serine/threonine kinase receptors. The tyrosine kinase receptors are characterised by an extracellular domain, a transmembrane domain, and an intracellular domain which possess tyrosine kinase activity. VEGFR, PDGFR, FGFR, CSF-1R and c-KIT are examples of tyrosine kinase growth factor receptors which also contain immunoglobulin domains in the extracellular portion. Dys-regulation of growth factor function results in many different disease phenotypes, including, but not exclusive to oncology (Bartucci M et al, (2001) Cancer Res. September 15;61(18):6747-54, Dias S et al., (2001) Proc Natl Acad Sci USA. September 11;98(19):10857-62, Djavan B et al., (2001) World J Urol. 19(4):225-33), inflammation (Fiocchi C. (2001) J Clin Invest. August;108(4):523-6, Hodge S et al., (2001) Respirology. September;6(3):205-211, Fenwick S A et al., (2001) J Anat. September;199(Pt 3):231-40), neurological (Cooper J D et al., (2001) Proc Natl Acad Sci USA 98(18):10439-44, Fahnestock M et al, (2001) Mol Cell Neurosci 18(2):210-20), and metabolism (Vickers M H et al., (2001) Endocrinology. 142(9):3964-73).        
TABLE 1Immunoglubulin domain-containing cell surface recognition moleculesReceptorLigandDistributionICAM-1LFA-1 (CD11a/CD18)Widespread, endothelial cells, fibroblasts,5 Ig domainsMac-1 (CD11b/CD18),epithelium, monocytes, lymphocytes, dendriticCD43cells, chondrocytes.ICAM-2LFA-1 (CD11b)endothelial cells (high): lymphocytes, monocytes,2 Ig domainsbasophils, platelets (low).ICAM-3LFA-1 (αd/CD 18)Lymphocytes, monocytes, neutrophils, eosinophils,5 Ig domainsbasophils.VCAM-1α4β1, α4β7Endothelial cells, monocytes, fibroblasts, dendritic6 or 7 Igcells, bone marrow stromal cells, myoblasts.domainsLFA-3CD2Endothelial cells, leukocytes, epithelial cells6 Ig domainsPECAM-1CD31, heparinEndothelial cells (at EC-EC junctions), T cell(CD31)subsets, platelets, neutrophils, eosinophils,monocytes, smooth muscle cells, bone marrowstem cells.NCAMNCAM, heparin SO4Neural cells, muscleMAdCAM-1α4β7, L-selectinPeyer's patch, mesenteric lymph nodes, mucosal4 Ig domainsendothelial cells, spleen.CD2CD58, CD59, CD48T lymphocytesVEGFRVEGFWidespread, retina, umbilical vein, adrenal, NT2neuronal precursor cellsFGFRFGFWidespread, brain, colon, ovaryKITStem Cell Factor, MGFWidespread, foetus, melanocytes, gall bladder,cerebellum, gastric epithelium (low)PDGFRPDGFWidespread, breast, placenta, fibroblast, lung,ovary, skin, heartCSF-1RCSFWidespread, placenta, liver, multiple sclerosislesions, spleen, lung, breast.Immunoglobulin domain-containing cell surface recognition molecules have thus been shown to play a role in diverse physiological functions, many of which can play a role in disease processes. Alteration of their activity is a means to alter the disease phenotype and as such identification of novel Immunoglobulin domain-containing cell surface recognition molecules is highly relevant as they may play a role in many diseases, particularly immunology, inflammatory disease, oncology, cardiovascular disease, central nervous system disorders and infection.